I guess great minds think alike. My setup is similar (though not exactly the same) on my PC. I set it up under the guidelines of what would be the most efficient way to cool it and maintain airflow. I think I'll use what's in the link to modify my setup a little bit.

I'm no expert on cooling but wouldn't having top and rear only result in a negatively pressurized case and excessive dust accumulation in the case cracks? If you left all the unused ports open then that would probably not be an issue.

Also, did you cover the not in use ports? There becomes a much greater number of variations if you leave some uncovered without a fan vs covering all not in use. If you left them uncovered then it wouldn't be suprising that the two exhaust fan option at top and rear would be best, air would be flowing more quickly through the case due to lack of back pressure due to the large number of inlet ports. Since your top fan is so far forward (as compared to a bottom mount PSU) it's not suprising it took longer to stabilize temperature. Any flow from the front or bottom intakes would get distributed along a path between them and the top port, which pretty much doesn't intersect any of the components your trying to cool but pulls accumulated hot air from the top of the case.

Also on a bottom mount PSU I bet you'd get much better flow across the components since both the back and top would be closer to the corner opposite the front and bottom intakes.

The test needs to explain how much cfm intake and exhaust in each example. Positive vs negative pressure is an important point not covered. Thank you very much for doing this experiment, it's helps answer some questions, leaves some unanswered. Great start though, I wish I had a bunch of fans and some tools to drill holes in my case.